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Generated by SRI International Pathway Tools Version 25.0, Authors S Authors: Pallavi Subhraveti Ron Caspi Peter Midford Peter D Karp An online version of this diagram is available at BioCyc.org. Biosynthetic pathways are positioned in the left of the cytoplasm, degradative pathways on the right, and reactions not assigned to any pathway are in the far right of the cytoplasm. Transporters and membrane proteins are shown on the membrane. Ingrid Keseler Periplasmic (where appropriate) and extracellular reactions and proteins may also be shown. Pathways are colored according to their cellular function. Gcf_000686005Cyc: Phyllobacterium sp. UNC302MFCol5.2 Cellular Overview Connections between pathways are omitted for legibility. Anamika Kothari lipid II (meso diaminopimelate 3-O-L-lysyl-1-O- containing) phosphate phosphatidylglycerol FtsW RS0112300 MprF lipid II (meso 3-O-L-lysyl-1-O- diaminopimelate phosphatidylglycerol containing) phosphate Amino Acid Degradation Storage Compound Biosynthesis Polyprenyl Biosynthesis Hormone Biosynthesis Aromatic Compound Biosynthesis Macromolecule Modification tRNA-uridine 2-thiolation ATP N 6 -(3-methylbut- ditrans,octacis- ditrans,octacis- a 1-acyl-2- a [DNA]-3'- a 5'-phospho- a [protein]-L- and selenation (bacteria) an L-cysteinyl- 34 di-trans,poly-cis indole-3-acetate biosynthesis L-valine degradation I a sulfurated adenosylcobinamide a purine a [glutamine- an L-asparaginyl- a cytidine polyhydroxybutanoate biosynthesis chorismate biosynthesis I L-leucine degradation I L-arginine degradation V L-histidine degradation II L-tryptophan degradation to 2-en-1-yl)- undecaprenyldiphospho- undecaprenyldiphospho- arachidonoyl- hydroxyl [DNA] Asn Cys lys methionine L-tyrosine degradation I ATP [tRNA ] [tRNA ] ATP roseoflavin Ile2 Metabolic Regulator Biosynthesis -undecaprenyl biosynthesis 3-(4-hydroxyphenyl) Alcohol Degradation [sulfur carrier] 37 ribonucleoside synthetase]- in tRNA peptide- (arginine deiminase pathway) 2-amino-3-carboxymuconate adenosine N-acetyl-(N- N-acetyl-(N- sn-glycerol 5'-phosphate Aminoacyl-tRNA Charging glutaminyl-tRNA gln biosynthesis via transamidation phosphate biosynthesis IV (bacteria) D-erythrose pyruvate biosynthesis cys in tRNA 5'-triphosphate acetylglucosaminyl) acetylglucosaminyl) 3-phosphate CTP L-tyrosine methionine acetyl-CoA ADP val semialdehyde ATP-dependent ppGpp metabolism (2E,6E)-farnesyl (indol-3-yl) 4-phosphate leu tyr his glycerol and glycerophosphodiester degradation muramoyl-L-alanyl-γ- muramoyl-L-alanyl- (S)-S-oxide glycine betaine IPP 3-deoxy-7- cysteine ATP synthase arg aminoacyl-tRNA aminoacyl-tRNA tRNA diphosphate acetonitrile histidine trp tRNA (N6-isopentenyl bifunctional β γ DNA ligase: bifunctional reductase acetyl-CoA C- nitrile phosphoheptulonate tyr branched-chain branched-chain bifunctional D-isoglutaminyl-N-( - -D-isoglutaminyl- phosphatidate bifunctional [glutamine hydrolase: hydrolase: lysidine(34) glu biosynthesis I (Gram- desulfurase: subunit C: adenosine(37)-C2)- adenosylcobinamide BR48_RS0114820 MsrA: msrA pppGpp acetyltransferase: hydratase: bifunctional amino acid aspartate arginine ammonia- tryptophan 2,3- glycerol D-asparaginyl)-L-lysyl- N-(β-D-asparaginyl) synthetase] BR48_RS0122835 BR48_RS0122835 riboflavin kinase/ synthetase negative bacteria) synthase class II: sufS BR48_RS25055 amino acid methylthiotransferase kinase/ cytidylyltransferase: BR48_RS0105330 isoprenyl nthB nthA aspartate aminotransferase: transaminase/ deiminase: lyase: hutH dioxygenase: D-alanyl-D-alanine -L-lysyl-D-alanine adenylyltransferase/ cisplatin damage FAD synthetase: TilS: tilS peptide- (indol-3-yl) 3-deoxy- BR48_RS0113025 cysteine desulfurase: [+ 7 isozymes] aminotransferase: urocanate MiaB: miaB adenosylcobinamide- BR48_RS0118130 aminoacyl-tRNA aminoacyl-tRNA choline [+ 2 isozymes] transferase: transaminase/ BR48_RS0122710 aspartate 4- arcA kynA L-proline degradation I [glutamine synthetase]- response ATP- BR48_RS0104475 methionine D-arabino- ATP BR48_RS0122710 N-Formyl-L- phosphate phosphatidate hydrolase: hydrolase: bifunctional (p)ppGpp choline acetamide BR48_RS0111395 succinate adenylyl-L-tyrosine dependent BR48_RS0118125 aspartate 4- decarboxylase: urocanate kynurenine a glycerophosphodiester 34 (S)-S-oxide dehydrogenase: heptulosonate an [L-cysteine branched-chain branched-chain guanylyltransferase: monofunctional monofunctional cytidylyltransferase: BR48_RS0108530 BR48_RS0108530 a lysidine synthetase/guanosine- acetoacetyl-CoA amidase: decarboxylase: BR48_RS0118820 L-citrulline dehydrogenase, phosphorylase: DNA ligase: roseoflavin reductase an L-glutamyl- 7-phosphate desulfurase]-S- amino acid amino acid hydratase: pro glycerol cobU biosynthetic biosynthetic BR48_RS0110235 in tRNA Ile2 3',5'-bis(diphosphate) 3'- betA di-trans,octa-cis BR48_RS0115470 BR48_RS0118820 hydrophobic BR48_RS0102920 BR48_RS0116220 adenine MsrA: msrA [tRNA Gln ] 3-dehydroquinate sulfanyl-L-cysteine aminotransferase: aminotransferase: bifunctional BR48_RS0106840 peptidoglycan peptidoglycan a protein-L- pyrophosphohydrolase: betaine aldehyde -undecaprenyl [+ 2 isozymes] bifunctional glycerophosphodiester membrane anchor adenosyl- dinucleotide synthase: bifunctional BR48_RS0103245 4-methyl-2-BR48_RS0103245 aspartate 4-imidazolone- transglycosylase: transglycosylase: tRNA Asn a tRNA Cys Asp-tRNA(Asn) BR48_RS0102465 diphosphate ornithine proline glycerol kinase phosphodiesterase: protein: sdhD cobinamide a CDP-1-acyl- asn cys methionine- betaine-aldehyde aspartate 5-propanoate mtgA mtgA a [glutamine /Glu-tRNA(Gln) (3R)-3- undecaprenyl- (indol-3-yl)acetate BR48_RS0110835 3-methyl-2- oxopentanoate transaminase/ carbamoyltransferase: L-kynurenine dehydrogenase/L- GlpK: glpK BR48_RS0118090 phosphate a purine 2-arachidonoyl- [DNA] (S)-S-oxide dehydrogenase: transaminase/ 6 synthetase]-O gln amidotransferase hydroxybutanoyl- poly-[(R)-3- diphosphate a [TusA sulfur- oxobutanoate aspartate 4- argF imidazolonepropionase: glutamate gamma- N -(3-methylbut- ribonucleoside glycerol betB 3-dehydroquinate aspartate 4- 5'-deoxyadenosine an unsulfurated 4 -(5'-adenylyl) subunit GatB: gatB CoA hydroxybutanoate] phosphatase: carrier protein]-S- decarboxylase: BR48_RS0106825 semialdehyde 2-en-1-yl)-2- met 5'-diphosphate a peptidoglycan di-trans,octa-cis a peptidoglycan di-trans,octa-cis GTP ppGpp 3-(4- [sulfur carrier] -L-tyrosine Asp-tRNA(Asn) decarboxylase: sulfanyl-L-cysteine BR48_RS0112475 sn-glycerol 3-phosphate (methylsulfanyl) dimer (E. faeciums) -undecaprenyl dimer (E. faecium -undecaprenyl Asp-tRNA(Asn) glycine betaine BR48_RS0108145 type II 3- carbamoyl dehydrogenase 3-(4- BR48_RS0112475 3-methylbutanoyl- hydroxyphenyl) N-formimino- 37 /Glu-tRNA(Gln) class I poly(R)- di-trans,octa-cis dehydroquinate L-ornithine PutA: putA adenosine diphosphate , tetrapeptide) diphosphate /Glu-tRNA(Gln) hydroxyphenyl) CoA pyruvate phosphate L-glutamate (S)-1-pyrroline- glycerol-3-phosphate amidotransferase nucleoside- bifunctional (p)ppGpp hydroxyalkanoic -undecaprenyl dehydratase: aroQ isobutanoyl-CoA 3-hydroxy- in tRNA amidotransferase: pyruvate isovaleryl-CoA glutamine- 5-carboxylate dehydrogenase: subunit GatB: gatB diphosphate kinase: synthetase/guanosine- acid synthase: phosphate 4-hydroxyphenylpyruvate formimidoylglutamate L-kynurenine gatC gatA a [TusD sulfur- BR48_RS0107715 [+ 7 isozymes] phaC 3-dehydroshikimate dehydrogenase: dioxygenase: hppD hydrolyzing deiminase: F0F1 ATP a 5-phosphooxy- BR48_RS0102030 3',5'-bis(diphosphate) 3'- + + carrier protein]-S- BR48_RS0102795 carbamoyl- kynureninase: ditrans,octacis- a peptidoglycan with an [HPr]- phosphoenol a carboxy- a mature a [glutamine 4-methyl-5-(2- L-rhamnulose succinate (E)-4-hydroxy-3- a protein-L- H H pyrophosphohydrolase: BR48_RS0106820 menadione NADH H + synthase ammonium L-glutamyl- shikimate sulfanyl-L-cysteine kynU DHAP undecaprenyldiphospho- (L-alanyl-γ-D-glutamyl- adenylated- cys peptidoglycan synthetase]-O phosphooxyethyl) 1-phosphate methylbut-2-en- methionine- poly-[(R)-3- 3-methylcrotonyl- homogentisate phosphate L-histidine pyruvate (n) HMP-PP semialdehyde ATP [tRNA Gln ] BR48_RS0102465 dehydrogenase: N-formyl- β 4 thiazole 1-yl diphosphate synthase: L-glutamate-5- N-acetyl-(N-acetyl- -D- L-lysyl-D-alanyl-D- [ThiS sulfur- (meso-DAP -(5'-adenylyl) NAD-dependent biotin flavodoxin- (R)-S-oxide hydroxybutanoate] methylacrylyl-CoA CoA 3-hydroxyanthranilate peptide- BR48_RS0108640 homogentisate carA carB L-glutamate semialdehyde Aromatic Compound glucosaminyl)muramoyl- alanine) pentapeptide carrier protein] containing) -L-tyrosine succinate- a reduced Asp-tRNA(Asn) methylcrotonoyl- phosphoenolpyruvate- bifunctional dependent methionine a [TusE sulfur enoyl-CoA 1,2-dioxygenase: N-formylglutamate Degradation L-alanyl-γ-D-glutamyl-L- NADH-quinone semialdehyde H O c-type thiamine (E)-4-hydroxy- (R)-S-oxide 2 /Glu-tRNA(Gln) GDP shikimate CoA carboxylase: BR48_RS0116270 carbamate bifunctional lysyl-D-alanyl-D-alanine -protein oxidoreductase: rhamnulose-1- dehydrogenase: biotin--[acetyl-CoA- 34 carrier protein]-S hydratase: amidohydrolase: lytic phosphate 3-methylbut- cytochrome amidotransferase a uridine in tRNA BR48_RS0102800 proline 4-hydroxyphenylacetate phosphotransferase: ptsP cysteine desulfurase: BR48_RS0117355 bifunctional [glutamine phosphate aldolase/ reductase RS0119895 an oxidized -sulfanylcysteine BR48_RS0117195 4-maleyl- BR48_RS0110080 synthase: BR48_RS0116570 carboxylase] ligase: subunit GatB: gatB shikimate kinase: [+ 2 isozymes] dehydrogenase/L- degradation BR48_RS0111395 transglycosylase synthetase] short-chain 2-enyl- MsrB: msrB O c-type acetoacetate 2-amino-3- phosphoenolpyruvate-
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